PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures.

Establishing a link between RNA structure and function remains a great challenge in RNA biology. The emergence of high-throughput structure profiling experiments is revolutionizing our ability to decipher structure, yet principled approaches for extracting information on structural elements directly from these data sets are lacking. We present PATTERNA, an unsupervised pattern recognition algorithm that rapidly mines RNA structure motifs from profiling data. We demonstrate that PATTERNA detects motifs with an accuracy comparable to commonly used thermodynamic models and highlight its utility in automating data-directed structure modeling from large data sets. PATTERNA is versatile and compatible with diverse profiling techniques and experimental conditions

Efficient Learning of Sparse Conditional Random Fields for Supervised Sequence Labelling

Conditional Random Fields (CRFs) constitute a popular and efficient approach for supervised sequence labelling. CRFs can cope with large description spaces and can integrate some form of structural dependency between labels. In this contribution, we address the issue of efficient feature selection for CRFs based on imposing sparsity through an L1 penalty. We first show how sparsity of the parameter set can be exploited to significantly speed up training and labelling. We then introduce coordinate descent parameter update schemes for CRFs with L1 regularization. We finally provide some empirical comparisons of the proposed approach with state-of-the-art CRF training strategies. In particular, it is shown that the proposed approach is able to take profit of the sparsity to speed up processing and hence potentially handle larger dimensional models

Recommending Structured Objects: Paths and Sets

Recommender systems have been widely adopted in industry to help people find the most appropriate items to purchase or consume from the increasingly large collection of available resources (e.g., books, songs and movies). Conventional recommendation techniques follow the approach of ``ranking all possible options and pick the top'', which can work effectively for single item recommendation but fall short when the item in question has internal structures. For example, a travel trajectory with a sequence of points-of-interest or a music playlist with a set of songs. Such structured objects pose critical challenges to recommender systems due to the intractability of ranking all possible candidates. This thesis study the problem of recommending structured objects, in particular, the recommendation of path (a sequence of unique elements) and set (a collection of distinct elements). We study the problem of recommending travel trajectories in a city, which is a typical instance of path recommendation. We propose methods that combine learning to rank and route planning techniques for efficient trajectory recommendation. Another contribution of this thesis is to develop the structured recommendation approach for path recommendation by substantially modifying the loss function, the learning and inference procedures of structured support vector machines. A novel application of path decoding techniques helps us achieve efficient learning and recommendation. Additionally, we investigate the problem of recommending a set of songs to form a playlist as an example of the set recommendation problem. We propose to jointly learn user representations by employing the multi-task learning paradigm, and a key result of equivalence between bipartite ranking and binary classification enables efficient learning of our set recommendation method. Extensive evaluations on real world datasets demonstrate the effectiveness of our proposed approaches for path and set recommendation

Convolutional Codes in Rank Metric with Application to Random Network Coding

Random network coding recently attracts attention as a technique to disseminate information in a network. This paper considers a non-coherent multi-shot network, where the unknown and time-variant network is used several times. In order to create dependencies between the different shots, particular convolutional codes in rank metric are used. These codes are so-called (partial) unit memory ((P)UM) codes, i.e., convolutional codes with memory one. First, distance measures for convolutional codes in rank metric are shown and two constructions of (P)UM codes in rank metric based on the generator matrices of maximum rank distance codes are presented. Second, an efficient error-erasure decoding algorithm for these codes is presented. Its guaranteed decoding radius is derived and its complexity is bounded. Finally, it is shown how to apply these codes for error correction in random linear and affine network coding.Comment: presented in part at Netcod 2012, submitted to IEEE Transactions on Information Theor

An intelligent information forwarder for healthcare big data systems with distributed wearable sensors

© 2016 IEEE. An increasing number of the elderly population wish to live an independent lifestyle, rather than rely on intrusive care programmes. A big data solution is presented using wearable sensors capable of carrying out continuous monitoring of the elderly, alerting the relevant caregivers when necessary and forwarding pertinent information to a big data system for analysis. A challenge for such a solution is the development of context-awareness through the multidimensional, dynamic and nonlinear sensor readings that have a weak correlation with observable human behaviours and health conditions. To address this challenge, a wearable sensor system with an intelligent data forwarder is discussed in this paper. The forwarder adopts a Hidden Markov Model for human behaviour recognition. Locality sensitive hashing is proposed as an efficient mechanism to learn sensor patterns. A prototype solution is implemented to monitor health conditions of dispersed users. It is shown that the intelligent forwarders can provide the remote sensors with context-awareness. They transmit only important information to the big data server for analytics when certain behaviours happen and avoid overwhelming communication and data storage. The system functions unobtrusively, whilst giving the users peace of mind in the knowledge that their safety is being monitored and analysed